The reasons for this are many, but two stick out. First of all, it makes life easier for most consumers if apps are in one place. Windows Mobile had tens of thousands of apps over the years, but they were available from the developer or from aggregation sites like Handango. None of those were easy to find for the average phone user so the third party draw of WinMo wasn't that great.
Another reason is Microsoft can control the quality of the apps. No, I don't mean that every app you buy will be a superb app, but you can be reasonably sure that it won't have a virus and shouldn't be able to have access to confidential information on your device without your express permission. Should any app that breaks the rules make it through, Microsoft can press a kill switch removing the app from devices worldwide, protecting the consumer.
With ChevronWP7 though, users can now bypass all of that if desired. There are certain instances where this is handy without having to pay the fee to the Marketplace to unlock your device as a developer, but it does have risks. Those that like to tinker with their devices will enjoy the increased access ChevronWP7 gives them, but the average person probably won't have a reason to bother with it. Whether Microsoft will take action to try and undo this is as of yet unknown. They have released an official response, which WinRumors has posted. In essence, they prefer you to use your phone as intended and any unlocking software could void the warranty, render the phone unusable or block access to some or all online services the device relies on, like Windows Live.
On the custom ROM front though, Microsoft appears to have taken a definitive stance rather than just issue a dire warning to users. MobileCrunch has posted that Windows Phone 7 has a little bit of "Microsoft Genuine Advantage" special sauce baked in. If certain registry keys don't specifically match the hardware you are using, the platform will block access to online services like Windows Live. Without that, you have no access to Hotmail, the Marketplace, Xbox Live games, Zune and possibly more. Without those, the phone is far less functional than intended.
The point to all of this is, just like hacking any mobile phone today, do so at your own risk. You run the gamut from having irritating little issues to contend with to having a shiny paperweight for your desk.